Genome analysis of sponge symbiont ‘Candidatus Halichondribacter symbioticus’ shows genomic adaptation to a host-dependent lifestyle

Abstract

The marine sponge Halichondria panicea inhabits coastal areas around the globe and is a widely studied sponge species in terms of its biology, yet the ecological functions of its dominant bacterial symbiont ‘Candidatus Halichondribacter symbioticus’ remain unknown. Here, we present the draft genome of ‘Ca. H. symbioticus’ HS1 (2.8 Mbp, ca. 87.6% genome coverage) recovered from the sponge metagenome of H. panicea in order to study functions and symbiotic interactions at the genome level. Functional genome comparison of HS1 against closely related free-living seawater bacteria revealed a reduction of genes associated with carbohydrate transport and transcription regulation, pointing towards a limited carbohydrate metabolism, and static transcriptional dynamics reminiscent of other bacterial symbionts. In addition, HS1 was enriched in sponge symbiont specific gene families related to host–symbiont interactions and defence. Similarity in the functional gene repertoire between HS1 and a phylogenetically more distant symbiont in the marine sponge Aplysina aerophoba, based on COG category distribution, suggest a convergent evolution of symbiont specific traits and general metabolic features. This warrants further investigation into convergent genomic evolution of symbionts across different sponge species and habitats.